Two deleted scenes from the pilot episode are included on this DVD set. The episode can be played optionally with or without the deleted scenes included. The first deleted scene shows Dana Scully's boyfriend, Ethan Minette, at work in a television studio, talking with Scully before she leaves Washington D.C. to investigate a case in Oregon with Fox Mulder. In the second deleted scene, Scully and her boyfriend lie together in bed, after Scully has returned from Oregon, as Scully receives a phone call from Mulder. This "deleted" scene is actually a larger version of a scene included in the pilot as it was televised but shows Scully's boyfriend lying next to her.

Fox Home Entertainment re-released every season of The X-Files on Region 1 DVD in 2006 in slimmer packaging. However, some discs were omitted therefore some special features listed above may not be present on the newer Region 1 Sets. Fox Home Entertainment also re-released the The X-Files on Region 2 DVD in slimmer packaging in late 2004/early 2005, the content was exactly the same as the original releases.